What is happening here is that the modes are assigned numbers so that we can consistently refer to a single mode across frequencies.
At every frequency the *.out file will list the modes of that frequency in order of Modal Significance. The mode tracking algorithm will however determine mode numbering. In your example of getting modes in order 3-2-1, that simply means that at this frequency mode 3 is the most significant followed by mode 2 then lastly mode 1.
When you request 6 modes you will only receive results for 6 modes at every frequency, but you will receive the most significant 6 modes at that frequency. This means that over the requested frequency range some modes will fall out of significance and new modes will enter significance. It is then very possible for a mode with the number 'mode 100' to be in the top 6 most significant modes at a later frequency.
If you would like the modes numbered 1 to 6 at every frequency you can disable tracking in the *.pre file. The easiest way is to use EDITFEKO. The CMA request will look something like this:
** Characteristic modes
OM: 6 : 1 : -1 ** CharacteristicModes1
With the last number indicating that tracking is disabled.
The Characteristic Mode formulation for dielectrics solved with the surface equivalence principle (SEP) results in a set of eigen modes that contains both internal and external resonances. The internal modes (sometimes call non-physical or fictitious) do not radiate any power, and are thus removed from the result set. It is advised to increase the number of modes requested when dealing with such models.